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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgcatgatcctgtgatcacagtattattcttatctgtttagattttaagtgacttttttatttatactttctttttcttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC

Basic information

species Vitis vinifera
transcript Vv10s0003g02830.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g44040.2 (Oryza sativa), 3'ss of exon 10
gtaagttgcatgatcctgtgatcacagtattattcttatctgtttagattttaagtgacttttttatttatactttcttttt-cttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC
||||||||||| ||||            || | ||   |||||      | ||  | |  ||   | | || |      |   ||  || |||    ||  |||       | |||   |      ||| ||| ||||||||||| || || |||||||| || |||||| ||||||| || |||| |||||| ||||||||||||||||| || ||
gtaagttgcattatcc------------ataagtcccctctgt----gctctacattaaattagcaatgatgcacggagtagactgcttattaaccattccttt------ttgctccacctc----agGCTGGCTATTTGTGGTACGAGTATATTTACAAACTAGACAAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCAC

upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 10
------------------------gtaagttgcatgatcctgtgatcacagtattattcttatctg-tttagattttaagtgacttttttatttatactttctttttctttt--ttttagtttttaatttaattgtctactctgtcctctat---agGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC
                         |     |  |     | |  |||   |   || ||| | || ||||     ||  |    ||||  |||| ||  |  |  | | ||  ||| |  |  |    ||| |      ||||| |   ||   ||| ||||||  | ||||||||||| || |||| ||| |||||| ||||||| || |||| |||||||||||| ||||||||||| || ||
gtaagttgcatccatcttttaccaatgcacagactttctatattgtcaagatgacatacttgtttgctttaccaactagatttgcttttgttttaaaccatgatgctgtattgatttcaaatgctgtactaactaggacttctgttcctcattttagGCTGGTTACCTATGGTATGAATATATCTACAGGCTAGACAAAATTACATACAACAAGTACCATCCCTACACGTCATGGATTCCTATCAC

upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 5
gtaagttgcatgatcctgtgatcacagtattattcttatctgtttagattttaagtgacttttttatttatactttctttttcttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC
||||||| |   |  || | | |   ||  |  |   | |||||  |||||      |     |  || | ||     | || ||  |  |   |  | | |   |  | |  |   || ||||  |||||| | | ||||||||||||| || |||||||| |||||||||||||| || |||| ||||||||||||||||||||| || |||||
gtaagttcccacaatctcttacctttgttgttgtggaaactgtt-ggatttctttaaatcaagtacttgacaccactgtgttgttaatactg--tactgactaggtgttgtgtttcttcttcta--gGTTGGCTTTCTGTGGTATGAATATATATACAAGCTAGACAAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAAC

upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 10
gtaagttgcatgatcctgtgatcacagtattattct--tatctgtttagattttaagtgacttttttatttatactttctttttcttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC
||||||| ||||||| | |  |  |||| ||  |    |  ||     || |||||| ||  |  |||  || | |||  | ||| || || |||                                  |  || ||| ||||||| ||||| || |||||||||||||||  ||||||||| |||| |||||||||||| || ||||||||||||||
gtaagttccatgatcttctcttgccagtgttgatgcactgactaggatgagtttaag-gaaatgattaactacaattttctgttcattcttctag-

upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 11
gtaagttgcatgatcctgtgatcacagtatt-attcttatctgtttagattttaagtgacttttttatttatactttctttttctt---ttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC
|| |||| |||  || |   || | | |||| ||  || ||| ||    | ||| || | |  || | |  | |||  | |         |   ||      ||  |   | | |  | | || | | |||||||| || ||||||||||||||||| |||||||||||||| ||  |||| || ||| |||| |||||||| || ||||||||||| ||
gtgagttacatc-tcttacaataagattattcatggttttctattctcctgttatgttattacttcaatattccttgatgtagaccaaaatgggtaaacaagaacatctctttttcatttttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATACAACAAGCTCCACCCCTACACCTCTTGGATTCCAATTAC

upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 11
gtaagttgcatgatcctgtgatcacagtattattcttatctgttta-gattttaagtgacttttttat-ttat-actttctttttcttttttttagtttttaat---ttaa----------ttgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC
|| |||| |||| || |   || | | ||||         | || | | ||||   |     |||||| |||| ||||   | ||||||  | |||     |||   | ||          |  | |  ||| || | | |||||||| || ||||||||||||||||| ||||||||||| || ||  |||| || ||| |||| |||||||| |||||||||||||| ||
gtgagttacatg-tcttacaataagattatttgctaagattattcatggttttctattctccttttatgttattacttcaatattctttgatgtagaccaaaatgggtaaacaagaacatctcttttcatctttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGATAAGGTCTCATACAACAAGCTCCACCCCTACACCTCATGGATTCCAATTAC

upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G34410.3 (Arabidopsis thaliana), 3'ss of exon 10
gtaagttgcatgatcctgtgatcacagtattattcttatctgtttagattttaagtgacttttttatttatactttctttttcttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC
                                      |  |||| | || |   || ||| |  || | || | | |||    || || |  |    || ||  ||  |||   ||| |     ||||||||||  | |||||||||||||| |||||||| ||||| |||||||| || || |  |||||||||||||| ||||||||||||||
-------------------------------------gtgagtttgggttctctctggcttatggatct-ta-tgtatttgatattattctgatgcccaagttg-ttccctatattgttc-----agGTTGGTTACCTATGGTATGAATACATATACAAGCTTGACAAGGTTACATACAACAAATATCATCCCTACACATCGTGGATTCCAATAAC

upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttgcatgatcctgtgatcacagtattattcttatctgtttagattttaagtgacttttttatttatactttctttttcttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC
                          ||    |  |    | | | |  ||   ||    |  | || |||| | |  |   |  || ||  | | ||  | |  | || | |    |  ||   ||| ||||||  | |||||||||||||| |||||||||||||| ||||| || || || |  |||||||||||||| ||||||||||||||
--------------------------gtgagttgttagcttttctcggcttctggt----tcatcatatatagtcttctccacaattattctgatgtttgtgtcgtggttt-ccaaatgttc---agGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctttttcttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC
                                    tctactctgtcctct  CT-rich tract
     tttttcttttttttag  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgcatgatcctgtgatcacagtattattcttatctgtttagattttaagtgacttttttatttatactttctttttcttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA